Andrew G. McArthur
Andrew G. McArthur
https://www.ncbi.nlm.nih.gov/pubmed/30365026?dopt=Abstract Victors: a web-based knowledge base of virulence factors in human and animal pathogens.
@danielhhaft we've been reviewing [Identification of 76 novel B1 metallo-β-lactamases through large-scale screening of genomic and metagenomic data](https://pubmed.ncbi.nlm.nih.gov/29020980/). The authors identify 77 putative beta-lactamases by using novel HMMs. Attached are...
[OXA-116](https://card.mcmaster.ca/ontology/37841) is a partial gene in CARD but listed at [NCBI's Reference Gene Catalog](https://www.ncbi.nlm.nih.gov/pathogens/refgene/#oxa-116). @danielhhaft do you have additional data on this gene or perhaps partials are not supported in...
From @iorga to @arpcard @agmcarthur @danielhhaft: > I saw that in the last NCBI/CARD update there were many additions and some changes regarding the OXY enzymes. Maybe that you are...
The MEGARes team (@Isabella136) has been reviewing CARD curation and has a list of errors for @arpcard to inspect: https://github.com/Isabella136/AmrPlusPlus_SNP/blob/in-depth/genes-issues.md
Two entries in the Galaxy Toolshed: * https://toolshed.g2.bx.psu.edu/view/card/rgi/84bd24ac33fd * https://toolshed.g2.bx.psu.edu/view/card/rgi/a5a3c70913e99d57 Plus two RGI repos: * https://github.com/arpcard/rgi_wrapper * https://github.com/arpcard/rgi_database_builder @arpcard please review and update to support latest version of RGI.
Analysis of simulated validation data by the CARD team (unpublished) revealed that Prodigal undercalls ORFs when the _-split_prodigal_jobs_ option is used. This was particularly noticeable in a _Acinetobacter baumannii_ genomic...
Generate a verbose README on the output files from individual assemblies, summaries among assemblies, ncov-tools, etc. Consider making a corresponding YouTube video.
CARD is starting to curated sub-families of beta-lactamases into the ARO, but we should also start to curate sub-groups of beta-lactams, e.g., more specific groupings than just `cephalosporin`. Starting this...
Playing with some bait-capture enriched ARG metagenomics data with _RGI bwt_ with _KMA_ and all the _wildcard variants_ and looking at the gene level report, I found tet(Q) with **All...